DOI: 10.1093/bioinformatics/btk023. OPM: Orientations of Proteins in Membranes database

OPM: Orientations of Proteins in Membranes database

10.1093/bioinformatics/btk023

Crossref journal-article

Oxford University Press (OUP)

Bioinformatics (286)

Abstract

Abstract Summary: The Orientations of Proteins in Membranes (OPM) database provides a collection of transmembrane, monotopic and peripheral proteins from the Protein Data Bank whose spatial arrangements in the lipid bilayer have been calculated theoretically and compared with experimental data. The database allows analysis, sorting and searching of membrane proteins based on their structural classification, species, destination membrane, numbers of transmembrane segments and subunits, numbers of secondary structures and the calculated hydrophobic thickness or tilt angle with respect to the bilayer normal. All coordinate files with the calculated membrane boundaries are available for downloading. Availabililty: Contact: almz@umich.edu

Bibliography

Lomize, M. A., Lomize, A. L., Pogozheva, I. D., & Mosberg, H. I. (2006). OPM: Orientations of Proteins in Membranes database. Bioinformatics, 22(5), 623â625.

Authors 4

Mikhail A. Lomize (first)
Andrei L. Lomize (additional)
Irina D. Pogozheva (additional)
Henry I. Mosberg (additional)

References 15 Referenced 1,067

10.1093/nar/gkh039 / Nucleic Acids Res. / SCOP database in 2004: refinements integrate structure and sequence family data by Andreeva (2004)
10.1016/S1093-3263(03)00122-0 / J. Mol. Graph. Model. / Insertion of X-ray structures of proteins in membranes by Basyn (2003)
10.1093/nar/28.1.235 / Nucleic Acids Res. / The Protein Data Bank by Berman (2000)
10.1385/MB:27:3:253 / Mol. Biotechnol. / The IUBMB-endorsed transporter classification system by Busch (2004)
10.1096/fasebj.12.13.1281 / FASEB J. / Cys-scanning mutagenesis: a novel approach to structure function relationships in polytopic membrane proteins by Frillingos (1998)
10.1016/S0968-0004(98)01253-5 / Trends Biochem. Sci. / PQS: a protein quaternary structure file server by Henrick (1998)
10.1016/S0065-3233(03)63010-X / Adv. Protein Chem. / Rhodopsin structure, dynamics, and activation: a perspective from crystallography, site-directed spin labeling, sulfhydryl reactivity, and disulfide cross-linking by Hubbell (2003)
10.1110/ps.43501 / Protein Sci. / MPtopo: A database of membrane protein topology by Jayasinghe (2001)
10.1016/S0005-2736(03)00056-7 / Biochim. Biophys. Acta. / Lipid–protein interactions in biological membranes: a structural perspective by Lee (2003)
10.1146/annurev.biophys.34.040204.144534 / Ann. Rev. Biophys. Biomol. Struct. / Use of EPR power saturation to analyze the membrane-docking geometries of peripheral proteins: applications to C2 domains by Malmberg (2005)
10.1146/annurev.bi.58.070189.003135 / Annu. Rev. Biochem. / The bacterial photosynthetic reaction center as a model for membrane proteins by Rees (1989)
10.1093/bioinformatics/bth340 / Bioinformatics / Transmembrane proteins in the Protein Data Bank: identification and classification by Tusnady (2004)
10.1093/nar/gki002 / Nucleic Acids Res. / PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank by Tusnady (2005)
10.1016/S0968-0004(97)89047-0 / Trends Biochem. Sci. / WebMol—a Java-based PDB viewer by Walther (1997)
{'key': '2023012408515535400_b15', 'first-page': '397', 'article-title': 'Precise annotation of transmembrane segments with garlic—a free molecular visualization program', 'volume': '77', 'author': 'Zucic', 'year': '2004', 'journal-title': 'Croat. Chem. Acta'} / Croat. Chem. Acta / Precise annotation of transmembrane segments with garlic—a free molecular visualization program by Zucic (2004)

Dates

Type	When
Created	19 years, 7 months ago (Jan. 5, 2006, 8:39 p.m.)
Deposited	2 years, 7 months ago (Jan. 24, 2023, 4:27 a.m.)
Indexed	1 day, 2 hours ago (Aug. 29, 2025, 6:34 a.m.)
Issued	19 years, 7 months ago (Jan. 5, 2006)
Published	19 years, 7 months ago (Jan. 5, 2006)
Published Online	19 years, 7 months ago (Jan. 5, 2006)
Published Print	19 years, 5 months ago (March 1, 2006)

Funders 0

None

BibTeX

@article{Lomize_2006, title={OPM: Orientations of Proteins in Membranes database}, volume={22}, ISSN={1367-4803}, url={http://dx.doi.org/10.1093/bioinformatics/btk023}, DOI={10.1093/bioinformatics/btk023}, number={5}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Lomize, Mikhail A. and Lomize, Andrei L. and Pogozheva, Irina D. and Mosberg, Henry I.}, year={2006}, month=jan, pages={623–625} }

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